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3. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author

Meng, Bo, Kemp, Steven A, Papa, Guido, Datir, Rawlings, Ferreira, Isabella ATM, Marelli, Sara, Harvey, William T, Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A, Mlcochova, Petra, Consortium, The COVID-19 Genomics UK, Robson, Samuel C, Loman, Nicholas J, Connor, Thomas R, Golubchik, Tanya, Nunez, Rocio T Martinez, Ludden, Catherine, Corden, Sally, Johnston, Ian, Bonsall, David, Smith, Colin P, Awan, Ali R, Bucca, Giselda, Torok, M Estee, Saeed, Kordo, Prieto, Jacqui A, Jackson, David K, Hamilton, William L, Snell, Luke B, Moore, Catherine, Harrison, Ewan M, Goncalves, Sonia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Livett, Rich, Moses, Samuel, Amato, Roberto, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Barrett, Jeff, Aanensen, David M, Curran, Martin D, Parmar, Surendra, Aggarwal, Dinesh, Shepherd, James G, Parker, Matthew D, Glaysher, Sharon, Bashton, Matthew, Underwood, Anthony P, Pacchiarini, Nicole, Loveson, Katie F, Templeton, Kate E, Langford, Cordelia F, Sillitoe, John, de Silva, Thushan I, Wang, Dennis, Kwiatkowski, Dominic, Rambaut, Andrew, O’Grady, Justin, Cottrell, Simon, Holden, Matthew TG, Thomson, Emma C, Osman, Husam, Andersson, Monique, Chauhan, Anoop J, Hassan-Ibrahim, Mohammed O, Lawniczak, Mara, Alderton, Alex, Chand, Meera, Constantinidou, Chrystala, Unnikrishnan, Meera, Darby, Alistair C, Hiscox, Julian A, Paterson, Steve, Martincorena, Inigo, Volz, Erik M, Page, Andrew J, Pybus, Oliver G, Bassett, Andrew R, Ariani, Cristina V, Chapman, Michael H Spencer, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, Taha, Yusri, McHugh, Martin P, Dewar, Rebecca, Jahun, Aminu S, McMurray, Claire, Pandey, Sarojini, McKenna, James P, Nelson, Andrew, Young, Gregory R, McCann, Clare M, and Elliott, Scott

Subjects
Emerging Infectious Diseases, Infectious Diseases, Lung, Pneumonia, Good Health and Well Being, Animals, Antibodies, Neutralizing, Antibodies, Viral, COVID-19, Cell Line, Chlorocebus aethiops, HEK293 Cells, Humans, Immune Evasion, Mutation, Pandemics, Phylogeny, Protein Binding, Recurrence, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vero Cells, COVID-19 Genomics UK (COG-UK) Consortium, Alpha variant, B.1.1.7, antibody escape, deletion, infectivity, neutralizing antibodies, resistance, spike mutation, Biochemistry and Cell Biology, Medical Physiology
Abstract

We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.

Published
2021

5. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity

Author

Meng, Bo, Abdullahi, Adam, Ferreira, Isabella A. T. M., Goonawardane, Niluka, Saito, Akatsuki, Kimura, Izumi, Yamasoba, Daichi, Gerber, Pehuén Pereyra, Fatihi, Saman, Rathore, Surabhi, Zepeda, Samantha K., Papa, Guido, Kemp, Steven A., Ikeda, Terumasa, Toyoda, Mako, Tan, Toong Seng, Kuramochi, Jin, Mitsunaga, Shigeki, Ueno, Takamasa, Shirakawa, Kotaro, Takaori-Kondo, Akifumi, Brevini, Teresa, Mallery, Donna L., Charles, Oscar J., Bowen, John E., Joshi, Anshu, Walls, Alexandra C., Jackson, Laurelle, Martin, Darren, Smith, Kenneth G. C., Bradley, John, Briggs, John A. G., Choi, Jinwook, Madissoon, Elo, Meyer, Kerstin B., Mlcochova, Petra, Ceron-Gutierrez, Lourdes, Doffinger, Rainer, Teichmann, Sarah A., Fisher, Andrew J., Pizzuto, Matteo S., de Marco, Anna, Corti, Davide, Hosmillo, Myra, Lee, Joo Hyeon, James, Leo C., Thukral, Lipi, Veesler, David, Sigal, Alex, Sampaziotis, Fotios, Goodfellow, Ian G., Matheson, Nicholas J., Sato, Kei, and Gupta, Ravindra K.

Published
2022
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8. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author

Robson, Samuel C., Loman, Nicholas J., Connor, Thomas R., Golubchik, Tanya, Martinez Nunez, Rocio T., Ludden, Catherine, Corden, Sally, Johnston, Ian, Bonsall, David, Smith, Colin P., Awan, Ali R., Bucca, Giselda, Torok, M. Estee, Saeed, Kordo, Prieto, Jacqui A., Jackson, David K., Hamilton, William L., Snell, Luke B., Moore, Catherine, Harrison, Ewan M., Goncalves, Sonia, Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Livett, Rich, Moses, Samuel, Amato, Roberto, Nicholls, Sam, Bull, Matthew, Smith, Darren L., Barrett, Jeff, Aanensen, David M., Curran, Martin D., Parmar, Surendra, Aggarwal, Dinesh, Shepherd, James G., Parker, Matthew D., Glaysher, Sharon, Bashton, Matthew, Underwood, Anthony P., Pacchiarini, Nicole, Loveson, Katie F., Templeton, Kate E., Langford, Cordelia F., Sillitoe, John, de Silva, Thushan I., Wang, Dennis, Kwiatkowski, Dominic, Rambaut, Andrew, O’Grady, Justin, Cottrell, Simon, Holden, Matthew T.G., Thomson, Emma C., Osman, Husam, Andersson, Monique, Chauhan, Anoop J., Hassan-Ibrahim, Mohammed O., Lawniczak, Mara, Alderton, Alex, Chand, Meera, Constantinidou, Chrystala, Unnikrishnan, Meera, Darby, Alistair C., Hiscox, Julian A., Paterson, Steve, Martincorena, Inigo, Volz, Erik M., Page, Andrew J., Pybus, Oliver G., Bassett, Andrew R., Ariani, Cristina V., Chapman, Michael H. Spencer, Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Taha, Yusri, McHugh, Martin P., Dewar, Rebecca, Jahun, Aminu S., McMurray, Claire, Pandey, Sarojini, McKenna, James P., Nelson, Andrew, Young, Gregory R., McCann, Clare M., Elliott, Scott, Lowe, Hannah, Temperton, Ben, Roy, Sunando, Price, Anna, Rey, Sara, Wyles, Matthew, Rooke, Stefan, Shaaban, Sharif, de Cesare, Mariateresa, Letchford, Laura, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Hosmillo, Myra, O’Toole, Áine, Hesketh, Andrew R., Stark, Richard, du Plessis, Louis, Ruis, Chris, Adams, Helen, Bourgeois, Yann, Michell, Stephen L., Grammatopoulos, Dimitris, Edgeworth, Jonathan, Breuer, Judith, Todd, John A., Fraser, Christophe, Buck, David, John, Michaela, Kay, Gemma L., Palmer, Steve, Peacock, Sharon J., Heyburn, David, Weldon, Danni, Robinson, Esther, McNally, Alan, Muir, Peter, Vipond, Ian B., Boyes, John, Sivaprakasam, Venkat, Salluja, Tranprit, Dervisevic, Samir, Meader, Emma J., Park, Naomi R., Oliver, Karen, Jeffries, Aaron R., Ott, Sascha, da Silva Filipe, Ana, Simpson, David A., Williams, Chris, Masoli, Jane A.H., Knight, Bridget A., Jones, Christopher R., Koshy, Cherian, Ash, Amy, Casey, Anna, Bosworth, Andrew, Ratcliffe, Liz, Xu-McCrae, Li, Pymont, Hannah M., Hutchings, Stephanie, Berry, Lisa, Jones, Katie, Halstead, Fenella, Davis, Thomas, Holmes, Christopher, Iturriza-Gomara, Miren, Lucaci, Anita O., Randell, Paul Anthony, Cox, Alison, Madona, Pinglawathee, Harris, Kathryn Ann, Brown, Julianne Rose, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa Louise, Liggett, Steven, Graham, Clive, Swindells, Emma, Collins, Jennifer, Eltringham, Gary, Campbell, Sharon, McClure, Patrick C., Clark, Gemma, Sloan, Tim J., Jones, Carl, Lynch, Jessica, Warne, Ben, Leonard, Steven, Durham, Jillian, Williams, Thomas, Haldenby, Sam T., Storey, Nathaniel, Alikhan, Nabil-Fareed, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Perry, Malorie, Craine, Noel, Lyons, Ronan A., Beckett, Angela H., Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Davies, Robert, Blane, Beth, Girgis, Sophia T., Beale, Mathew A., Bellis, Katherine L., Dorman, Matthew J., Drury, Eleanor, Kane, Leanne, Kay, Sally, McGuigan, Samantha, Nelson, Rachel, Prestwood, Liam, Rajatileka, Shavanthi, Batra, Rahul, Williams, Rachel J., Kristiansen, Mark, Green, Angie, Justice, Anita, Mahanama, Adhyana I.K., Samaraweera, Buddhini, Hadjirin, Nazreen F., Quick, Joshua, Poplawski, Radoslaw, Kermack, Leanne M., Reynolds, Nicola, Hall, Grant, Chaudhry, Yasmin, Pinckert, Malte L., Georgana, Iliana, Moll, Robin J., Thornton, Alicia, Myers, Richard, Stockton, Joanne, Williams, Charlotte A., Yew, Wen C., Trotter, Alexander J., Trebes, Amy, MacIntyre-Cockett, George, Birchley, Alec, Adams, Alexander, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Hilvers, Ember, Jones, Hannah, Asad, Hibo, Coombes, Jason, Evans, Johnathan M., Fina, Laia, Gilbert, Lauren, Graham, Lee, Cronin, Michelle, Kumziene-Summerhayes, Sara, Taylor, Sarah, Jones, Sophie, Groves, Danielle C., Zhang, Peijun, Gallis, Marta, Louka, Stavroula F., Starinskij, Igor, Jackson, Chris, Gourtovaia, Marina, Tonkin-Hill, Gerry, Lewis, Kevin, Tovar-Corona, Jaime M., James, Keith, Baxter, Laura, Alam, Mohammad T., Orton, Richard J., Hughes, Joseph, Vattipally, Sreenu, Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Boyd, Olivia, Geidelberg, Lily, Zarebski, Alex E., Raghwani, Jayna, Kraemer, Moritz U.G., Southgate, Joel, Lindsey, Benjamin B., Freeman, Timothy M., Keatley, Jon-Paul, Singer, Joshua B., de Oliveira Martins, Leonardo, Yeats, Corin A., Abudahab, Khalil, Taylor, Ben E.W., Menegazzo, Mirko, Danesh, John, Hogsden, Wendy, Eldirdiri, Sahar, Kenyon, Anita, Mason, Jenifer, Robinson, Trevor I., Holmes, Alison, Price, James, Hartley, John A., Curran, Tanya, Mather, Alison E., Shankar, Giri, Jones, Rachel, Howe, Robin, Morgan, Sian, Wastenge, Elizabeth, Chapman, Michael R., Mookerjee, Siddharth, Stanley, Rachael, Smith, Wendy, Peto, Timothy, Eyre, David, Crook, Derrick, Vernet, Gabrielle, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Guest, Martyn, Munn, Robert, Bradley, Declan T., Wyatt, Tim, Beaver, Charlotte, Foulser, Luke, Palmer, Sophie, Churcher, Carol M., Brooks, Ellena, Smith, Kim S., Galai, Katerina, McManus, Georgina M., Bolt, Frances, Coll, Francesc, Meadows, Lizzie, Attwood, Stephen W., Davies, Alisha, De Lacy, Elen, Downing, Fatima, Edwards, Sue, Scarlett, Garry P., Jeremiah, Sarah, Smith, Nikki, Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Wantoch, Michelle, Jamrozy, Dorota, Lo, Stephanie, Patel, Minal, Hill, Verity, Bewshea, Claire M., Ellard, Sian, Auckland, Cressida, Harrison, Ian, Bishop, Chloe, Chalker, Vicki, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Hopes, Richard, Asamaphan, Patawee, Niebel, Marc O., Gunson, Rory N., Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Carden, Holli, Machin, Nicholas W., Jackson, Kathryn A., Ahmad, Shazaad S.Y., George, Ryan P., Turtle, Lance, O’Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Alcolea-Medina, Adela, Charalampous, Themoula, Patel, Amita, Levett, Lisa J., Heaney, Judith, Rowan, Aileen, Taylor, Graham P., Shah, Divya, Atkinson, Laura, Lee, Jack C.D., Westhorpe, Adam P., Jannoo, Riaz, Lowe, Helen L., Karamani, Angeliki, Ensell, Leah, Chatterton, Wendy, Pusok, Monika, Dadrah, Ashok, Symmonds, Amanda, Sluga, Graciela, Molnar, Zoltan, Baker, Paul, Bonner, Stephen, Essex, Sarah, Barton, Edward, Padgett, Debra, Scott, Garren, Greenaway, Jane, Payne, Brendan A.I., Burton-Fanning, Shirelle, Waugh, Sheila, Raviprakash, Veena, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, Moore, Jonathan, Stonehouse, Susanne, Smith, Louise, Davidson, Rose K., Bedford, Luke, Coupland, Lindsay, Wright, Victoria, Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Khakh, Manjinder, Fleming, Vicki M., Lister, Michelle M., Howson-Wells, Hannah C., Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Duckworth, Nichola, Walsh, Sarah, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Kidd, Stephen, Williams, Rebecca, Gifford, Laura, Bicknell, Kelly, Wyllie, Sarah, Lloyd, Allyson, Impey, Robert, Malone, Cassandra S., Cogger, Benjamin J., Levene, Nick, Monaghan, Lynn, Keeley, Alexander J., Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Betteridge, Emma, Farr, Ben W., Goodwin, Scott, Quail, Michael A., Scott, Carol, Shirley, Lesley, Thurston, Scott A.J., Rajan, Diana, Bronner, Iraad F., Aigrain, Louise, Redshaw, Nicholas M., Lensing, Stefanie V., McCarthy, Shane, Makunin, Alex, Balcazar, Carlos E., Gallagher, Michael D., Williamson, Kathleen A., Stanton, Thomas D., Michelsen, Michelle L., Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W., Sambles, Christine M., Studholme, David J., Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Schaefer, Ulf, Groves, Natalie, Gallagher, Eileen, Lee, David, Williams, David, Ellaby, Nicholas, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Ledesma, Juan, Twohig, Katherine A., Allara, Elias, Pearson, Clare, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Brown, Paul E., Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen N., Smollett, Katherine L., Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Nickbakhsh, Seema, Vamos, Edith E., Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Gregory, Richard, Gemmell, Matthew, Wierzbicki, Claudia, Webster, Hermione J., Fisher, Chloe L., Signell, Adrian W., Betancor, Gilberto, Wilson, Harry D., Nebbia, Gaia, Flaviani, Flavia, Cerda, Alberto C., Merrill, Tammy V., Wilson, Rebekah E., Cotic, Marius, Bayzid, Nadua, Thompson, Thomas, Acheson, Erwan, Rushton, Steven, O’Brien, Sarah, Baker, David J., Rudder, Steven, Aydin, Alp, Sang, Fei, Debebe, Johnny, Francois, Sarah, Vasylyeva, Tetyana I., Zamudio, Marina Escalera, Gutierrez, Bernardo, Marchbank, Angela, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, Morgan, Mari, Beer, Robert, Afifi, Safiah, Workman, Trudy, Fuller, William, Bresner, Catherine, Angyal, Adrienn, Green, Luke R., Parsons, Paul J., Tucker, Rachel M., Brown, Rebecca, Whiteley, Max, Bonfield, James, Puethe, Christoph, Whitwham, Andrew, Liddle, Jennifier, Rowe, Will, Siveroni, Igor, Le-Viet, Thanh, Gaskin, Amy, Johnson, Rob, Abnizova, Irina, Ali, Mozam, Allen, Laura, Anderson, Ralph, Ariani, Cristina, Austin-Guest, Siobhan, Bala, Sendu, Barrett, Jeffrey, Bassett, Andrew, Battleday, Kristina, Beal, James, Beale, Mathew, Bellany, Sam, Bellerby, Tristram, Bellis, Katie, Berger, Duncan, Berriman, Matt, Bevan, Paul, Binley, Simon, Bishop, Jason, Blackburn, Kirsty, Boughton, Nick, Bowker, Sam, Brendler-Spaeth, Timothy, Bronner, Iraad, Brooklyn, Tanya, Buddenborg, Sarah Kay, Bush, Robert, Caetano, Catarina, Cagan, Alex, Carter, Nicola, Cartwright, Joanna, Monteiro, Tiago Carvalho, Chapman, Liz, Chillingworth, Tracey-Jane, Clapham, Peter, Clark, Richard, Clarke, Adrian, Clarke, Catriona, Cole, Daryl, Cook, Elizabeth, Coppola, Maria, Cornell, Linda, Cornwell, Clare, Corton, Craig, Crackett, Abby, Cranage, Alison, Craven, Harriet, Craw, Sarah, Crawford, Mark, Cutts, Tim, Dabrowska, Monika, Davies, Matt, Dawson, Joseph, Day, Callum, Densem, Aiden, Dibling, Thomas, Dockree, Cat, Dodd, David, Dogga, Sunil, Dorman, Matthew, Dougan, Gordon, Dougherty, Martin, Dove, Alexander, Drummond, Lucy, Dudek, Monika, Durrant, Laura, Easthope, Elizabeth, Eckert, Sabine, Ellis, Pete, Farr, Ben, Fenton, Michael, Ferrero, Marcella, Flack, Neil, Fordham, Howerd, Forsythe, Grace, Francis, Matt, Fraser, Audrey, Freeman, Adam, Galvin, Anastasia, Garcia-Casado, Maria, Gedny, Alex, Girgis, Sophia, Glover, James, Gould, Oliver, Gray, Andy, Gray, Emma, Griffiths, Coline, Gu, Yong, Guerin, Florence, Hamilton, Will, Hanks, Hannah, Harrison, Ewan, Harrott, Alexandria, Harry, Edward, Harvison, Julia, Heath, Paul, Hernandez-Koutoucheva, Anastasia, Hobbs, Rhiannon, Holland, Dave, Holmes, Sarah, Hornett, Gary, Hough, Nicholas, Huckle, Liz, Hughes-Hallet, Lena, Hunter, Adam, Inglis, Stephen, Iqbal, Sameena, Jackson, Adam, Jackson, David, Verdejo, Carlos Jimenez, Jones, Matthew, Kallepally, Kalyan, Kay, Keely, Keatley, Jon, Keith, Alan, King, Alison, Kitchin, Lucy, Kleanthous, Matt, Klimekova, Martina, Korlevic, Petra, Krasheninnkova, Ksenia, Lane, Greg, Langford, Cordelia, Laverack, Adam, Law, Katharine, Lensing, Stefanie, Lewis-Wade, Amanah, Liddle, Jennifer, Lin, Quan, Lindsay, Sarah, Linsdell, Sally, Long, Rhona, Lovell, Jamie, Lovell, Jon, Mack, James, Maddison, Mark, Makunin, Aleksei, Mamun, Irfan, Mansfield, Jenny, Marriott, Neil, Martin, Matt, Mayho, Matthew, McClintock, Jo, McHugh, Sandra, MapcMinn, Liz, Meadows, Carl, Mobley, Emily, Moll, Robin, Morra, Maria, Morrow, Leanne, Murie, Kathryn, Nash, Sian, Nathwani, Claire, Naydenova, Plamena, Neaverson, Alexandra, Nerou, Ed, Nicholson, Jon, Nimz, Tabea, Noell, Guillaume G., O’Meara, Sarah, Ohan, Valeriu, Olney, Charles, Ormond, Doug, Oszlanczi, Agnes, Pang, Yoke Fei, Pardubska, Barbora, Park, Naomi, Parmar, Aaron, Patel, Gaurang, Payne, Maggie, Peacock, Sharon, Petersen, Arabella, Plowman, Deborah, Preston, Tom, Quail, Michael, Rance, Richard, Rawlings, Suzannah, Redshaw, Nicholas, Reynolds, Joe, Reynolds, Mark, Rice, Simon, Richardson, Matt, Roberts, Connor, Robinson, Katrina, Robinson, Melanie, Robinson, David, Rogers, Hazel, Rojo, Eduardo Martin, Roopra, Daljit, Rose, Mark, Rudd, Luke, Sadri, Ramin, Salmon, Nicholas, Saul, David, Schwach, Frank, Seekings, Phil, Simms, Alison, Sinnott, Matt, Sivadasan, Shanthi, Siwek, Bart, Sizer, Dale, Skeldon, Kenneth, Skelton, Jason, Slater-Tunstill, Joanna, Sloper, Lisa, Smerdon, Nathalie, Smith, Chris, Smith, Christen, Smith, James, Smith, Katie, Smith, Michelle, Smith, Sean, Smith, Tina, Sneade, Leighton, Soria, Carmen Diaz, Sousa, Catarina, Souster, Emily, Sparkes, Andrew, Spencer-Chapman, Michael, Squares, Janet, Stanley, Robert, Steed, Claire, Stickland, Tim, Still, Ian, Stratton, Mike, Strickland, Michelle, Swann, Allen, Swiatkowska, Agnieszka, Sycamore, Neil, Swift, Emma, Symons, Edward, Szluha, Suzanne, Taluy, Emma, Tao, Nunu, Taylor, Katy, Taylor, Sam, Thompson, Stacey, Thompson, Mark, Thomson, Mark, Thomson, Nicholas, Thurston, Scott, Toombs, Dee, Topping, Benjamin, Tovar-Corona, Jaime, Ungureanu, Daniel, Uphill, James, Urbanova, Jana, Van, Philip Jansen, Vancollie, Valerie, Voak, Paul, Walker, Danielle, Walker, Matthew, Waller, Matt, Ward, Gary, Weatherhogg, Charlie, Webb, Niki, Wells, Alan, Wells, Eloise, Westwood, Luke, Whipp, Theo, Whiteley, Thomas, Whitton, Georgia, Widaa, Sara, Williams, Mia, Wilson, Mark, Wright, Sean, Meng, Bo, Kemp, Steven A., Papa, Guido, Datir, Rawlings, Ferreira, Isabella A.T.M., Marelli, Sara, Harvey, William T., Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A., Mlcochova, Petra, Duncan, Lidia M., Carabelli, Alessandro M., Kenyon, Julia C., Lever, Andrew M., De Marco, Anna, Saliba, Christian, Culap, Katja, Cameroni, Elisabetta, Matheson, Nicholas J., Piccoli, Luca, Corti, Davide, James, Leo C., Robertson, David L., Bailey, Dalan, and Gupta, Ravindra K.

Published
2021
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9. The recruitment of TRiC chaperonin in rotavirus viroplasms correlates with virus replication

Author

Vetter, Janine, primary, Papa, Guido, additional, Tobler, Kurt, additional, Rodriguez, Javier M., additional, Kley, Manuel, additional, Myers, Michael, additional, Wiesendanger, Mahesa, additional, Schraner, Elisabeth M., additional, Luque, Daniel, additional, Burrone, Oscar R., additional, Fraefel, Cornel, additional, and Eichwald, Catherine, additional

Published
2024
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10. The recruitment of TRiC chaperonin in rotavirus viroplasms correlates with virus replication

Author

University of Zurich, 0000-0003-4368-6869, 0000-0001-7221-6706, 0000-0003-0001-4843, Vetter, Janine, Papa, Guido, Tobler, Kurt, Rodríguez, Javier M., Kley, Manuel, Myers, Michael, Wiesendanger, Mahesa, Schraner, Elisabeth M, Luque, Daniel, Burrone, Oscar R, Fraefel, Cornel, Eichwald, Catherine, University of Zurich, 0000-0003-4368-6869, 0000-0001-7221-6706, 0000-0003-0001-4843, Vetter, Janine, Papa, Guido, Tobler, Kurt, Rodríguez, Javier M., Kley, Manuel, Myers, Michael, Wiesendanger, Mahesa, Schraner, Elisabeth M, Luque, Daniel, Burrone, Oscar R, Fraefel, Cornel, and Eichwald, Catherine

Abstract

Rotavirus (RV) replication takes place in the viroplasms, cytosolic inclusions that allow the synthesis of virus genome segments and their encapsidation in the core shell, followed by the addition of the second layer of the virion. The viroplasms are composed of several viral proteins, including NSP5, which serves as the main building block. Microtubules, lipid droplets, and miRNA-7 are among the host components recruited in viroplasms. We investigated the interaction between RV proteins and host components of the viroplasms by performing a pull-down assay of lysates from RV-infected cells expressing NSP5-BiolD2. Subsequent tandem mass spectrometry identified all eight subunits of the tailless complex polypeptide I ring complex (TRiC), a cellular chaperonin responsible for folding at least 10% of the cytosolic proteins. Our confirmed findings reveal that TRiC is brought into viroplasms and wraps around newly formed double-layered particles. Chemical inhibition of TRiC and silencing of its subunits drastically reduced virus progeny production. Through direct RNA sequencing, we show that TRiC is critical for RV replication by controlling dsRNA genome segment synthesis, particularly negative-sense single-stranded RNA. Importantly, cryo-electron microscopy analysis shows that TRiC inhibition results in defective virus particles lacking genome segments and polymerase complex (VP1/VP3). Moreover, TRiC associates with VP2 and NSP5 but not with VP1. Also, VP2 is shown to be essential for recruiting TRiC in viroplasms and preserving their globular morphology. This study highlights the essential role of TRiC in viroplasm formation and in facilitating virion assembly during the RV life cycle.

Published
2024

11. The recruitment of TRiC chaperonin in rotavirus viroplasms correlates with virus replication

Author

Lopez, Carolina B, Parker, John S, Lopez, C B ( Carolina B ), Parker, J S ( John S ), Vetter, Janine; https://orcid.org/0000-0003-4368-6869, Papa, Guido, Tobler, Kurt; https://orcid.org/0000-0002-0013-7993, Rodriguez, Javier M, Kley, Manuel, Myers, Michael, Wiesendanger, Mahesa, Schraner, Elisabeth M; https://orcid.org/0000-0003-4608-4812, Luque, Daniel, Burrone, Oscar R, Fraefel, Cornel; https://orcid.org/0000-0001-7221-6706, Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843, Lopez, Carolina B, Parker, John S, Lopez, C B ( Carolina B ), Parker, J S ( John S ), Vetter, Janine; https://orcid.org/0000-0003-4368-6869, Papa, Guido, Tobler, Kurt; https://orcid.org/0000-0002-0013-7993, Rodriguez, Javier M, Kley, Manuel, Myers, Michael, Wiesendanger, Mahesa, Schraner, Elisabeth M; https://orcid.org/0000-0003-4608-4812, Luque, Daniel, Burrone, Oscar R, Fraefel, Cornel; https://orcid.org/0000-0001-7221-6706, and Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843

Abstract

Rotavirus (RV) replication takes place in the viroplasms, cytosolic inclusions that allow the synthesis of virus genome segments and their encapsidation in the core shell, followed by the addition of the second layer of the virion. The viroplasms are composed of several viral proteins, including NSP5, which serves as the main building block. Microtubules, lipid droplets, and miRNA-7 are among the host components recruited in viroplasms. We investigated the interaction between RV proteins and host components of the viroplasms by performing a pull-down assay of lysates from RV-infected cells expressing NSP5-BiolD2. Subsequent tandem mass spectrometry identified all eight subunits of the tailless complex polypeptide I ring complex (TRiC), a cellular chaperonin responsible for folding at least 10% of the cytosolic proteins. Our confirmed findings reveal that TRiC is brought into viroplasms and wraps around newly formed double-layered particles. Chemical inhibition of TRiC and silencing of its subunits drastically reduced virus progeny production. Through direct RNA sequencing, we show that TRiC is critical for RV replication by controlling dsRNA genome segment synthesis, particularly negative-sense single-stranded RNA. Importantly, cryo-electron microscopy analysis shows that TRiC inhibition results in defective virus particles lacking genome segments and polymerase complex (VP1/VP3). Moreover, TRiC associates with VP2 and NSP5 but not with VP1. Also, VP2 is shown to be essential for recruiting TRiC in viroplasms and preserving their globular morphology. This study highlights the essential role of TRiC in viroplasm formation and in facilitating virion assembly during the RV life cycle. IMPORTANCE The replication of rotavirus takes place in cytosolic inclusions termed viroplasms. In these inclusions, the distinct 11 double-stranded RNA genome segments are co-packaged to complete a genome in newly generated virus particles. In this study, we show for the first ti

Published
2024

16. Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2

Author

Gaynor, Katherine U, Vaysburd, Marina, Harman, Maximilian AJ, Albecka, Anna, Jeffrey, Phillip, Beswick, Paul, Papa, Guido, Chen, Liuhong, Mallery, Donna, McGuinness, Brian, Van Rietschoten, Katerine, Stanway, Steven, Brear, Paul, Lulla, Aleksei, Ciazynska, Katarzyna, Chang, Veronica T, Sharp, Jo, Neary, Megan, Box, Helen, Herriott, Jo, Kijak, Edyta, Tatham, Lee, Bentley, Eleanor G, Sharma, Parul, Kirby, Adam, Han, Ximeng, Stewart, James P, Owen, Andrew, Briggs, John AG, Hyvönen, Marko, Skynner, Michael J, James, Leo C, Gaynor, Katherine U [0000-0003-0461-810X], Harman, Maximilian AJ [0000-0002-3667-5929], Papa, Guido [0000-0002-5215-0014], Chen, Liuhong [0000-0003-1776-3146], Mallery, Donna [0000-0003-2713-5215], Brear, Paul [0000-0002-4045-0474], Ciazynska, Katarzyna [0000-0002-9899-2428], Chang, Veronica T [0000-0001-7047-9019], Sharp, Jo [0000-0001-8482-5736], Stewart, James P [0000-0002-8928-2037], Owen, Andrew [0000-0002-9819-7651], Briggs, John AG [0000-0003-3990-6910], Hyvönen, Marko [0000-0001-8683-4070], Skynner, Michael J [0000-0001-6586-9055], James, Leo C [0000-0003-2131-0334], and Apollo - University of Cambridge Repository

Subjects
Male, Mice, Mesocricetus, SARS-CoV-2, Cricetinae, Spike Glycoprotein, Coronavirus, Animals, COVID-19, Mice, Transgenic, Peptides, Antiviral Agents, Antibodies
Abstract

COVID-19 has stimulated the rapid development of new antibody and small molecule therapeutics to inhibit SARS-CoV-2 infection. Here we describe a third antiviral modality that combines the drug-like advantages of both. Bicycles are entropically constrained peptides stabilized by a central chemical scaffold into a bi-cyclic structure. Rapid screening of diverse bacteriophage libraries against SARS-CoV-2 Spike yielded unique Bicycle binders across the entire protein. Exploiting Bicycles' inherent chemical combinability, we converted early micromolar hits into nanomolar viral inhibitors through simple multimerization. We also show how combining Bicycles against different epitopes into a single biparatopic agent allows Spike from diverse variants of concern (VoC) to be targeted (Alpha, Beta, Delta and Omicron). Finally, we demonstrate in both male hACE2-transgenic mice and Syrian golden hamsters that both multimerized and biparatopic Bicycles reduce viraemia and prevent host inflammation. These results introduce Bicycles as a potential antiviral modality to tackle new and rapidly evolving viruses.

Published
2023

17. Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2

Author

Gaynor, Katherine U., primary, Vaysburd, Marina, additional, Harman, Maximilian A. J., additional, Albecka, Anna, additional, Jeffrey, Phillip, additional, Beswick, Paul, additional, Papa, Guido, additional, Chen, Liuhong, additional, Mallery, Donna, additional, McGuinness, Brian, additional, Van Rietschoten, Katerine, additional, Stanway, Steven, additional, Brear, Paul, additional, Lulla, Aleksei, additional, Ciazynska, Katarzyna, additional, Chang, Veronica T., additional, Sharp, Jo, additional, Neary, Megan, additional, Box, Helen, additional, Herriott, Jo, additional, Kijak, Edyta, additional, Tatham, Lee, additional, Bentley, Eleanor G., additional, Sharma, Parul, additional, Kirby, Adam, additional, Han, Ximeng, additional, Stewart, James P., additional, Owen, Andrew, additional, Briggs, John A. G., additional, Hyvönen, Marko, additional, Skynner, Michael J., additional, and James, Leo C., additional

Published
2023
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21. Rotavirus spike protein VP4 mediates viroplasm assembly by association to actin filaments

Author

Vetter, Janine, Papa, Guido, Seyffert, Michael, Gunasekera, Kapila, De Lorenzo, Giuditta, Wiesendanger, Mahesa, Reymond, Jean-Louis, Fraefel, Cornel, Burrone, Oscar R, Eichwald, Catherine, University of Zurich, and López, Susana

Subjects
Rotavirus, rotavirus, spike-protein, viroplasm, VP4, reverse-genetics, actin, cytoskeleton, 10077 Institute of Veterinary Anatomy, Immunology, Virus Replication, Microbiology, Reverse Genetics, Rotavirus Infections, Actin Cytoskeleton, Lectins, Virology, Insect Science, Humans, 570 Life sciences, biology, Capsid Proteins, Viral Replication Compartments, 10244 Institute of Virology
Abstract

The formation of viroplasms is a well-conserved step in the rotavirus (RV) life cycle. In these structures, both virus genome replication and progeny assembly take place. A stabilized microtubule cytoskeleton and lipid droplets are required for the viroplasm formation, which involves several virus proteins. The viral spike protein VP4 has not previously been shown to have a direct role in viroplasm formation. However, it is involved with virus-cell attachment, endocytic internalization, and virion morphogenesis. Moreover, VP4 interacts with actin cytoskeleton components, mainly in processes involving virus entrance and egress, and thereby may have an indirect role in viroplasm formation. In this study, we used reverse genetics to construct a recombinant RV, rRV/VP4-BAP, which contains a biotin acceptor peptide (BAP) in the K145-G150 loop of the VP4 lectin domain, permitting live monitoring. The recombinant virus was replication competent but showed a reduced fitness. We demonstrate that rRV/VP4-BAP infection, as opposed to rRV/wt infection, did not lead to a reorganized actin cytoskeleton as viroplasms formed were insensitive to drugs that depolymerize actin and inhibit myosin. Moreover, wt VP4, but not VP4-BAP, appeared to associate with actin filaments. Similarly, VP4 in co-expression with NSP5 and NSP2 induced a significant increase in the number of viroplasm-like structures. Interestingly, a small peptide mimicking loop K145-G150 rescued the phenotype of rRV/VP4-BAP by increasing its ability to form viroplasms and hence, improve virus progeny formation. Collectively, these results provide a direct link between VP4 and the actin cytoskeleton to catalyze viroplasm assembly.IMPORTANCEThe spike protein VP4 participates in diverse steps of the rotavirus (RV) life cycle, including virus-cell attachment, internalization, modulation of endocytosis, virion morphogenesis, and virus egress. Using reverse genetics, we constructed for the first time a recombinant RV, rRV/VP4-BAP, harboring a heterologous peptide in the lectin domain (loop K145-G150) of VP4. The rRV/VP4-BAP was replication-competent but with reduced fitness due to a defect in the ability to reorganize the actin cytoskeleton, which affected the efficiency of viroplasm assembly. This defect was rescued by adding a permeable small-peptide mimicking the wild-type VP4 loop K145-G150. In addition to revealing a new role of VP4, our findings suggest that rRV harboring an engineered VP4 could be used as a new dual vaccination platform providing immunity against RV and additional heterologous antigens.

Published
2022
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22. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

Author

Mlcochova, Petra, Kemp, Steven A., Dhar, Mahesh Shanker, Papa, Guido, Meng, Bo, Ferreira, Isabella A. T. M., Datir, Rawlings, Collier, Dami A., Albecka, Anna, Singh, Sujeet, Pandey, Rajesh, Brown, Jonathan, Zhou, Jie, Goonawardane, Niluka, Mishra, Swapnil, Whittaker, Charles, Mellan, Thomas, Marwal, Robin, Datta, Meena, Sengupta, Shantanu, Ponnusamy, Kalaiarasan, Radhakrishnan, Venkatraman Srinivasan, Abdullahi, Adam, Charles, Oscar, Chattopadhyay, Partha, Devi, Priti, Caputo, Daniela, Peacock, Tom, Wattal, Chand, Goel, Neeraj, Satwik, Ambrish, Vaishya, Raju, Agarwal, Meenakshi, Chauhan, Himanshu, Dikid, Tanzin, Gogia, Hema, Lall, Hemlata, Verma, Kaptan, Singh, Manoj K., Soni, Namita, Meena, Namonarayan, Madan, Preeti, Singh, Priyanka, Sharma, Ramesh, Sharma, Rajeev, Kabra, Sandhya, Kumar, Sattender, Kumari, Swati, Sharma, Uma, Chaudhary, Urmila, Sivasubbu, Sridhar, Scaria, Vinod, Oberoi, J. K., Raveendran, Reena, Datta, S., Das, Saumitra, Maitra, Arindam, Chinnaswamy, Sreedhar, Biswas, Nidhan Kumar, Parida, Ajay, Raghav, Sunil K., Prasad, Punit, Sarin, Apurva, Mayor, Satyajit, Ramakrishnan, Uma, Palakodeti, Dasaradhi, Seshasayee, Aswin Sai Narain, Thangaraj, K., Bashyam, Murali Dharan, Dalal, Ashwin, Bhat, Manoj, Shouche, Yogesh, Pillai, Ajay, Abraham, Priya, Potdar, Varsha Atul, Cherian, Sarah S., Desai, Anita Sudhir, Pattabiraman, Chitra, Manjunatha, M. V., Mani, Reeta S., Udupi, Gautam Arunachal, Nandicoori, Vinay, Tallapaka, Karthik Bharadwaj, Sowpati, Divya Tej, Kawabata, Ryoko, Morizako, Nanami, Sadamasu, Kenji, Asakura, Hiroyuki, Nagashima, Mami, Yoshimura, Kazuhisa, Ito, Jumpei, Kimura, Izumi, Uriu, Keiya, Kosugi, Yusuke, Suganami, Mai, Oide, Akiko, Yokoyama, Miyabishara, Chiba, Mika, Saito, Akatsuki, Butlertanaka, Erika P., Tanaka, Yuri L., Ikeda, Terumasa, Motozono, Chihiro, Nasser, Hesham, Shimizu, Ryo, Yuan, Yue, Kitazato, Kazuko, Hasebe, Haruyo, Nakagawa, So, Wu, Jiaqi, Takahashi, Miyoko, Fukuhara, Takasuke, Shimizu, Kenta, Tsushima, Kana, Kubo, Haruko, Shirakawa, Kotaro, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Takaori-Kondo, Akifumi, Tokunaga, Kenzo, Ozono, Seiya, Baker, Stephen, Dougan, Gordon, Hess, Christoph, Kingston, Nathalie, Lehner, Paul J., Lyons, Paul A., Matheson, Nicholas J., Owehand, Willem H., Saunders, Caroline, Summers, Charlotte, Thaventhiran, James E. D., Toshner, Mark, Weekes, Michael P., Maxwell, Patrick, Shaw, Ashley, Bucke, Ashlea, Calder, Jo, Canna, Laura, Domingo, Jason, Elmer, Anne, Fuller, Stewart, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Jose, Sherly, Kourampa, Jenny, Meadows, Anne, O'Brien, Criona, Price, Jane, Publico, Cherry, Rastall, Rebecca, Ribeiro, Carla, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Bullman, Ben, Dunmore, Benjamin J., Fawke, Stuart, Graf, Stefan, Hodgson, Josh, Huang, Christopher, Hunter, Kelvin, Jones, Emma, Legchenko, Ekaterina, Matara, Cecilia, Martin, Jennifer, Mescia, Federica, O'Donnell, Ciara, Pointon, Linda, Pond, Nicole, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Treacy, Carmen, Tong, Zhen, Wood, Jennifer, Wylot, Marta, Bergamaschi, Laura, Betancourt, Ariana, Bower, Georgie, Cossetti, Chiara, De Sa, Aloka, Epping, Madeline, Gleadall, Nick, Grenfell, Richard, Hinch, Andrew, Huhn, Oisin, Jackson, Sarah, Jarvis, Isobel, Krishna, Ben, Lewis, Daniel, Marsden, Joe, Nice, Francesca, Okecha, Georgina, Omarjee, Ommar, Perera, Marianne, Potts, Martin, Richoz, Nathan, Romashova, Veronika, Yarkoni, Natalia Savinykh, Sharma, Rahul, Stefanucci, Luca, Stephens, Jonathan, Strezlecki, Mateusz, Turner, Lori, De Bie, Eckart M. D. D., Bunclark, Katherine, Josipovic, Masa, Mackay, Michael, Rossi, Sabrina, Selvan, Mayurun, Spencer, Sarah, Yong, Cissy, Allison, John, Butcher, Helen, Clapham-Riley, Debbie, Dewhurst, Eleanor, Furlong, Anita, Graves, Barbara, Gray, Jennifer, Ivers, Tasmin, Kasanicki, Mary, Le Gresley, Emma, Linger, Rachel, Meloy, Sarah, Muldoon, Francesca, Ovington, Nigel, Papadia, Sofia, Phelan, Isabel, Stark, Hannah, Stirrups, Kathleen E., Townsend, Paul, Walker, Neil, Webster, Jennifer, Scholtes, Ingrid, Hein, Sabine, King, Rebecca, Mavousian, Antranik, Lee, Joo Hyeon, Bassi, Jessica, Silacci-Fegni, Chiara, Saliba, Christian, Pinto, Dora, Irie, Takashi, Yoshida, Isao, Hamilton, William L., Sato, Kei, Bhatt, Samir, Flaxman, Seth, James, Leo C., Corti, Davide, Piccoli, Luca, Barclay, Wendy S., Rakshit, Partha, Agrawal, Anurag, Gupta, Ravindra K., (INSACOG), Indian SARS-CoV-2 Genomics Consortium, Consortium, Genotype to Phenotype Japan (G2P-Japan), Collaboration, CITIID-NIHR BioResource COVID-19, Gupta, Ravindra K [0000-0001-9751-1808], Apollo - University of Cambridge Repository, and Gupta, Ravindra K. [0000-0001-9751-1808]

Subjects
Male, COVID-19 Vaccines, medicine.drug_class, Health Personnel, India, Monoclonal antibody, Virus Replication, Antibodies, Cell Line, Cell Fusion, Immune system, 13/100, medicine, Humans, Neutralizing antibody, Antibodies, Neutralizing, Female, Kinetics, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vaccination, Immune Evasion, Neutralizing, 631/326/596/4130, Syncytium, Multidisciplinary, Cell fusion, biology, article, Vaccine efficacy, 631/250/254, Virology, Spike Glycoprotein, Coronavirus, 13/31, biology.protein, Antibody, Infection
Abstract

The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era., A study of SARS-CoV-2 variants examining their transmission, infectivity, and potential resistance to therapies provides insights into the biology of the Delta variant and its role in the global pandemic.

Published
2022
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23. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity

Author

80728270, Meng, Bo, Abdullahi, Adam, Ferreira, Isabella A. T. M., Goonawardane, Niluka, Saito, Akatsuki, Kimura, Izumi, Yamasoba, Daichi, Gerber, Pehuén Pereyra, Fatihi, Saman, Rathore, Surabhi, Zepeda, Samantha K., Papa, Guido, Kemp, Steven A., Ikeda, Terumasa, Toyoda, Mako, Tan, Toong Seng, Kuramochi, Jin, Mitsunaga, Shigeki, Ueno, Takamasa, Shirakawa, Kotaro, Takaori-Kondo, Akifumi, Brevini, Teresa, Mallery, Donna L., Charles, Oscar J., The CITIID-NIHR BioResource COVID-19 Collaboration, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen, John E., Joshi, Anshu, Walls, Alexandra C., Jackson, Laurelle, Martin, Darren, Smith, Kenneth G. C., Bradley, John, Briggs, John A. G., Choi, Jinwook, Madissoon, Elo, Meyer, Kerstin, Mlcochova, Petra, Ceron-Gutierrez, Lourdes, Doffinger, Rainer, Teichmann, Sarah A., Fisher, Andrew J., Pizzuto, Matteo S., de Marco, Anna, Corti, Davide, Hosmillo, Myra, Lee, Joo Hyeon, James, Leo C., Thukral, Lipi, Veesler, David, Sigal, Alex, Sampaziotis, Fotios, Goodfellow, Ian G., Matheson, Nicholas J., Sato, Kei, Gupta, Ravindra K., 80728270, Meng, Bo, Abdullahi, Adam, Ferreira, Isabella A. T. M., Goonawardane, Niluka, Saito, Akatsuki, Kimura, Izumi, Yamasoba, Daichi, Gerber, Pehuén Pereyra, Fatihi, Saman, Rathore, Surabhi, Zepeda, Samantha K., Papa, Guido, Kemp, Steven A., Ikeda, Terumasa, Toyoda, Mako, Tan, Toong Seng, Kuramochi, Jin, Mitsunaga, Shigeki, Ueno, Takamasa, Shirakawa, Kotaro, Takaori-Kondo, Akifumi, Brevini, Teresa, Mallery, Donna L., Charles, Oscar J., The CITIID-NIHR BioResource COVID-19 Collaboration, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen, John E., Joshi, Anshu, Walls, Alexandra C., Jackson, Laurelle, Martin, Darren, Smith, Kenneth G. C., Bradley, John, Briggs, John A. G., Choi, Jinwook, Madissoon, Elo, Meyer, Kerstin, Mlcochova, Petra, Ceron-Gutierrez, Lourdes, Doffinger, Rainer, Teichmann, Sarah A., Fisher, Andrew J., Pizzuto, Matteo S., de Marco, Anna, Corti, Davide, Hosmillo, Myra, Lee, Joo Hyeon, James, Leo C., Thukral, Lipi, Veesler, David, Sigal, Alex, Sampaziotis, Fotios, Goodfellow, Ian G., Matheson, Nicholas J., Sato, Kei, and Gupta, Ravindra K.

Abstract

The SARS-CoV-2 Omicron BA.1 variant emerged in 20211 and bears multiple spike mutations2. Here we show that Omicron spike has higher affinity for ACE2 compared to Delta as well as a marked change of antigenicity conferring significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lower airway organoids, lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared to Delta. Replication differences mapped to entry efficiency using spike pseudotyped virus (PV) assays. The defect for Omicron PV to enter specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and knock down of TMPRSS2 impacted Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways3 demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that promotes cell entry via plasma membrane fusion, with greater dependency on cell entry via the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was markedly impaired compared to the Delta spike. Omicron’s less efficient spike cleavage at S1/S2 is associated with shift in cellular tropism away from TMPRSS2 expressing cells, with implications for altered pathogenesis.

Published
2022

24. Rotavirus Spike Protein VP4 Mediates Viroplasm Assembly by Association to Actin Filaments

Author

López, Susana, López, S ( Susana ), Vetter, Janine, Papa, Guido, Seyffert, Michael; https://orcid.org/0000-0001-7483-2430, Gunasekera, Kapila; https://orcid.org/0000-0002-2570-531X, De Lorenzo, Giuditta; https://orcid.org/0000-0002-2736-8740, Wiesendanger, Mahesa, Reymond, Jean-Louis; https://orcid.org/0000-0003-2724-2942, Fraefel, Cornel; https://orcid.org/0000-0001-7221-6706, Burrone, Oscar R, Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843, López, Susana, López, S ( Susana ), Vetter, Janine, Papa, Guido, Seyffert, Michael; https://orcid.org/0000-0001-7483-2430, Gunasekera, Kapila; https://orcid.org/0000-0002-2570-531X, De Lorenzo, Giuditta; https://orcid.org/0000-0002-2736-8740, Wiesendanger, Mahesa, Reymond, Jean-Louis; https://orcid.org/0000-0003-2724-2942, Fraefel, Cornel; https://orcid.org/0000-0001-7221-6706, Burrone, Oscar R, and Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843

Abstract

Rotavirus (RV) viroplasms are cytosolic inclusions where both virus genome replication and primary steps of virus progeny assembly take place. A stabilized microtubule cytoskeleton and lipid droplets are required for the viroplasm formation, which involves several virus proteins. The viral spike protein VP4 has not previously been shown to have a direct role in viroplasm formation. However, it is involved with virus-cell attachment, endocytic internalization, and virion morphogenesis. Moreover, VP4 interacts with actin cytoskeleton components, mainly in processes involving virus entrance and egress, and thereby may have an indirect role in viroplasm formation. In this study, we used reverse genetics to construct a recombinant RV, rRV/VP4-BAP, that contains a biotin acceptor peptide (BAP) in the K145-G150 loop of the VP4 lectin domain, permitting live monitoring. The recombinant virus was replication competent but showed a reduced fitness. We demonstrate that rRV/VP4-BAP infection, as opposed to rRV/wt infection, did not lead to a reorganized actin cytoskeleton as viroplasms formed were insensitive to drugs that depolymerize actin and inhibit myosin. Moreover, wild-type (wt) VP4, but not VP4-BAP, appeared to associate with actin filaments. Similarly, VP4 in coexpression with NSP5 and NSP2 induced a significant increase in the number of viroplasm-like structures. Interestingly, a small peptide mimicking loop K145-G150 rescued the phenotype of rRV/VP4-BAP by increasing its ability to form viroplasms and hence improve virus progeny formation. Collectively, these results provide a direct link between VP4 and the actin cytoskeleton to catalyze viroplasm assembly. IMPORTANCE The spike protein VP4 participates in diverse steps of the rotavirus (RV) life cycle, including virus-cell attachment, internalization, modulation of endocytosis, virion morphogenesis, and virus egress. Using reverse genetics, we constructed for the first time a recombinant RV, rRV/VP4-BAP, harboring a

Published
2022

25. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the variant of concern lineage B.1.1.7

Author

Meng, Bo, Kemp, Steven A., Papa, Guido, Datir, Rawlings, Ferreira, Isabella ATM., Marelli, Sara, Harvey, William T., Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A., Mlcochova, Petra, Duncan, Lidia M., Carabelli, Alessandro M., Kenyon, Julia C., Lever, Andrew M., De Marco, Anna, Saliba, Christian, Culap, Katja, Cameroni, Elisabetta, Matheson, Nicholas J., Piccoli, Luca, Corti, Davide, James, Leo C., Robertson, David L., Bailey, Dalan, and Gupta, Ravindra K.

Subjects
body regions
Abstract

We report SARS-CoV-2 spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of the receptor binding motif replacements such as N439K and Y453F known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that whilst ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of S proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of H69 and V70 residues in B.1.1.7 spike (where ΔH69/V70 naturally occurs) impairs spike incorporation and entry efficiency of B.1.1.7 spike pseudotyped virus. B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.

Published
2021

29. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

Author

Mlcochova, Petra, Kemp, Steven A., Dhar, Mahesh Shanker, Papa, Guido, Meng, Bo, Ferreira, Isabella A. T. M., Datir, Rawlings, Collier, Dami A., Albecka, Anna, Singh, Sujeet, Pandey, Rajesh, Brown, Jonathan, Zhou, Jie, Goonawardane, Niluka, Mishra, Swapnil, Whittaker, Charles, Mellan, Thomas, Marwal, Robin, Datta, Meena, Sengupta, Shantanu, Ponnusamy, Kalaiarasan, Radhakrishnan, Venkatraman Srinivasan, Abdullahi, Adam, Charles, Oscar, Chattopadhyay, Partha, Devi, Priti, Caputo, Daniela, Peacock, Tom, Wattal, Chand, Goel, Neeraj, Satwik, Ambrish, Vaishya, Raju, Agarwal, Meenakshi, Chauhan, Himanshu, Dikid, Tanzin, Gogia, Hema, Lall, Hemlata, Verma, Kaptan, Singh, Manoj K., Soni, Namita, Meena, Namonarayan, Madan, Preeti, Singh, Priyanka, Sharma, Ramesh, Sharma, Rajeev, Kabra, Sandhya, Kumar, Sattender, Kumari, Swati, Sharma, Uma, Chaudhary, Urmila, Sivasubbu, Sridhar, Scaria, Vinod, Oberoi, J. K., Raveendran, Reena, Datta, S., Das, Saumitra, Maitra, Arindam, Chinnaswamy, Sreedhar, Biswas, Nidhan Kumar, Parida, Ajay, Raghav, Sunil K., Prasad, Punit, Sarin, Apurva, Mayor, Satyajit, Ramakrishnan, Uma, Palakodeti, Dasaradhi, Seshasayee, Aswin Sai Narain, Thangaraj, K., Bashyam, Murali Dharan, Dalal, Ashwin, Bhat, Manoj, Shouche, Yogesh, Pillai, Ajay, Abraham, Priya, Potdar, Varsha Atul, Cherian, Sarah S., Desai, Anita Sudhir, Pattabiraman, Chitra, Manjunatha, M. V., Mani, Reeta S., Udupi, Gautam Arunachal, Nandicoori, Vinay, Tallapaka, Karthik Bharadwaj, Sowpati, Divya Tej, Kawabata, Ryoko, Morizako, Nanami, Sadamasu, Kenji, Asakura, Hiroyuki, Nagashima, Mami, Yoshimura, Kazuhisa, Ito, Jumpei, Kimura, Izumi, Uriu, Keiya, Kosugi, Yusuke, Suganami, Mai, Oide, Akiko, Yokoyama, Miyabishara, Chiba, Mika, Saito, Akatsuki, Butlertanaka, Erika P., Tanaka, Yuri L., Ikeda, Terumasa, Motozono, Chihiro, Nasser, Hesham, Shimizu, Ryo, Yuan, Yue, Kitazato, Kazuko, Hasebe, Haruyo, Nakagawa, So, Wu, Jiaqi, Takahashi, Miyoko, Fukuhara, Takasuke, Shimizu, Kenta, Tsushima, Kana, Kubo, Haruko, Shirakawa, Kotaro, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Takaori-Kondo, Akifumi, Tokunaga, Kenzo, Ozono, Seiya, Baker, Stephen, Dougan, Gordon, Hess, Christoph, Kingston, Nathalie, Lehner, Paul J., Lyons, Paul A., Matheson, Nicholas J., Owehand, Willem H., Saunders, Caroline, Summers, Charlotte, Thaventhiran, James E. D., Toshner, Mark, Weekes, Michael P., Maxwell, Patrick, Shaw, Ashley, Bucke, Ashlea, Calder, Jo, Canna, Laura, Domingo, Jason, Elmer, Anne, Fuller, Stewart, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Jose, Sherly, Kourampa, Jenny, Meadows, Anne, O'Brien, Criona, Price, Jane, Publico, Cherry, Rastall, Rebecca, Ribeiro, Carla, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Bullman, Ben, Dunmore, Benjamin J., Fawke, Stuart, Graf, Stefan, Hodgson, Josh, Huang, Christopher, Hunter, Kelvin, Jones, Emma, Legchenko, Ekaterina, Matara, Cecilia, Martin, Jennifer, Mescia, Federica, O'Donnell, Ciara, Pointon, Linda, Pond, Nicole, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Treacy, Carmen, Tong, Zhen, Wood, Jennifer, Wylot, Marta, Bergamaschi, Laura, Betancourt, Ariana, Bower, Georgie, Cossetti, Chiara, De Sa, Aloka, Epping, Madeline, Gleadall, Nick, Grenfell, Richard, Hinch, Andrew, Huhn, Oisin, Jackson, Sarah, Jarvis, Isobel, Krishna, Ben, Lewis, Daniel, Marsden, Joe, Nice, Francesca, Okecha, Georgina, Omarjee, Ommar, Perera, Marianne, Potts, Martin, Richoz, Nathan, Romashova, Veronika, Yarkoni, Natalia Savinykh, Sharma, Rahul, Stefanucci, Luca, Stephens, Jonathan, Strezlecki, Mateusz, Turner, Lori, De Bie, Eckart M. D. D., Bunclark, Katherine, Josipovic, Masa, Mackay, Michael, Rossi, Sabrina, Selvan, Mayurun, Spencer, Sarah, Yong, Cissy, Allison, John, Butcher, Helen, Clapham-Riley, Debbie, Dewhurst, Eleanor, Furlong, Anita, Graves, Barbara, Gray, Jennifer, Ivers, Tasmin, Kasanicki, Mary, Le Gresley, Emma, Linger, Rachel, Meloy, Sarah, Muldoon, Francesca, Ovington, Nigel, Papadia, Sofia, Phelan, Isabel, Stark, Hannah, Stirrups, Kathleen E., Townsend, Paul, Walker, Neil, Webster, Jennifer, Scholtes, Ingrid, Hein, Sabine, King, Rebecca, Mavousian, Antranik, Lee, Joo Hyeon, Bassi, Jessica, Silacci-Fegni, Chiara, Saliba, Christian, Pinto, Dora, Irie, Takashi, Yoshida, Isao, Hamilton, William L., Sato, Kei, Bhatt, Samir, Flaxman, Seth, James, Leo C., Corti, Davide, Piccoli, Luca, Barclay, Wendy S., Rakshit, Partha, Agrawal, Anurag, Gupta, Ravindra K., Mlcochova, Petra, Kemp, Steven A., Dhar, Mahesh Shanker, Papa, Guido, Meng, Bo, Ferreira, Isabella A. T. M., Datir, Rawlings, Collier, Dami A., Albecka, Anna, Singh, Sujeet, Pandey, Rajesh, Brown, Jonathan, Zhou, Jie, Goonawardane, Niluka, Mishra, Swapnil, Whittaker, Charles, Mellan, Thomas, Marwal, Robin, Datta, Meena, Sengupta, Shantanu, Ponnusamy, Kalaiarasan, Radhakrishnan, Venkatraman Srinivasan, Abdullahi, Adam, Charles, Oscar, Chattopadhyay, Partha, Devi, Priti, Caputo, Daniela, Peacock, Tom, Wattal, Chand, Goel, Neeraj, Satwik, Ambrish, Vaishya, Raju, Agarwal, Meenakshi, Chauhan, Himanshu, Dikid, Tanzin, Gogia, Hema, Lall, Hemlata, Verma, Kaptan, Singh, Manoj K., Soni, Namita, Meena, Namonarayan, Madan, Preeti, Singh, Priyanka, Sharma, Ramesh, Sharma, Rajeev, Kabra, Sandhya, Kumar, Sattender, Kumari, Swati, Sharma, Uma, Chaudhary, Urmila, Sivasubbu, Sridhar, Scaria, Vinod, Oberoi, J. K., Raveendran, Reena, Datta, S., Das, Saumitra, Maitra, Arindam, Chinnaswamy, Sreedhar, Biswas, Nidhan Kumar, Parida, Ajay, Raghav, Sunil K., Prasad, Punit, Sarin, Apurva, Mayor, Satyajit, Ramakrishnan, Uma, Palakodeti, Dasaradhi, Seshasayee, Aswin Sai Narain, Thangaraj, K., Bashyam, Murali Dharan, Dalal, Ashwin, Bhat, Manoj, Shouche, Yogesh, Pillai, Ajay, Abraham, Priya, Potdar, Varsha Atul, Cherian, Sarah S., Desai, Anita Sudhir, Pattabiraman, Chitra, Manjunatha, M. V., Mani, Reeta S., Udupi, Gautam Arunachal, Nandicoori, Vinay, Tallapaka, Karthik Bharadwaj, Sowpati, Divya Tej, Kawabata, Ryoko, Morizako, Nanami, Sadamasu, Kenji, Asakura, Hiroyuki, Nagashima, Mami, Yoshimura, Kazuhisa, Ito, Jumpei, Kimura, Izumi, Uriu, Keiya, Kosugi, Yusuke, Suganami, Mai, Oide, Akiko, Yokoyama, Miyabishara, Chiba, Mika, Saito, Akatsuki, Butlertanaka, Erika P., Tanaka, Yuri L., Ikeda, Terumasa, Motozono, Chihiro, Nasser, Hesham, Shimizu, Ryo, Yuan, Yue, Kitazato, Kazuko, Hasebe, Haruyo, Nakagawa, So, Wu, Jiaqi, Takahashi, Miyoko, Fukuhara, Takasuke, Shimizu, Kenta, Tsushima, Kana, Kubo, Haruko, Shirakawa, Kotaro, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Takaori-Kondo, Akifumi, Tokunaga, Kenzo, Ozono, Seiya, Baker, Stephen, Dougan, Gordon, Hess, Christoph, Kingston, Nathalie, Lehner, Paul J., Lyons, Paul A., Matheson, Nicholas J., Owehand, Willem H., Saunders, Caroline, Summers, Charlotte, Thaventhiran, James E. D., Toshner, Mark, Weekes, Michael P., Maxwell, Patrick, Shaw, Ashley, Bucke, Ashlea, Calder, Jo, Canna, Laura, Domingo, Jason, Elmer, Anne, Fuller, Stewart, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Jose, Sherly, Kourampa, Jenny, Meadows, Anne, O'Brien, Criona, Price, Jane, Publico, Cherry, Rastall, Rebecca, Ribeiro, Carla, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Bullman, Ben, Dunmore, Benjamin J., Fawke, Stuart, Graf, Stefan, Hodgson, Josh, Huang, Christopher, Hunter, Kelvin, Jones, Emma, Legchenko, Ekaterina, Matara, Cecilia, Martin, Jennifer, Mescia, Federica, O'Donnell, Ciara, Pointon, Linda, Pond, Nicole, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Treacy, Carmen, Tong, Zhen, Wood, Jennifer, Wylot, Marta, Bergamaschi, Laura, Betancourt, Ariana, Bower, Georgie, Cossetti, Chiara, De Sa, Aloka, Epping, Madeline, Gleadall, Nick, Grenfell, Richard, Hinch, Andrew, Huhn, Oisin, Jackson, Sarah, Jarvis, Isobel, Krishna, Ben, Lewis, Daniel, Marsden, Joe, Nice, Francesca, Okecha, Georgina, Omarjee, Ommar, Perera, Marianne, Potts, Martin, Richoz, Nathan, Romashova, Veronika, Yarkoni, Natalia Savinykh, Sharma, Rahul, Stefanucci, Luca, Stephens, Jonathan, Strezlecki, Mateusz, Turner, Lori, De Bie, Eckart M. D. D., Bunclark, Katherine, Josipovic, Masa, Mackay, Michael, Rossi, Sabrina, Selvan, Mayurun, Spencer, Sarah, Yong, Cissy, Allison, John, Butcher, Helen, Clapham-Riley, Debbie, Dewhurst, Eleanor, Furlong, Anita, Graves, Barbara, Gray, Jennifer, Ivers, Tasmin, Kasanicki, Mary, Le Gresley, Emma, Linger, Rachel, Meloy, Sarah, Muldoon, Francesca, Ovington, Nigel, Papadia, Sofia, Phelan, Isabel, Stark, Hannah, Stirrups, Kathleen E., Townsend, Paul, Walker, Neil, Webster, Jennifer, Scholtes, Ingrid, Hein, Sabine, King, Rebecca, Mavousian, Antranik, Lee, Joo Hyeon, Bassi, Jessica, Silacci-Fegni, Chiara, Saliba, Christian, Pinto, Dora, Irie, Takashi, Yoshida, Isao, Hamilton, William L., Sato, Kei, Bhatt, Samir, Flaxman, Seth, James, Leo C., Corti, Davide, Piccoli, Luca, Barclay, Wendy S., Rakshit, Partha, Agrawal, Anurag, and Gupta, Ravindra K.

Published
2021

30. A recombinant rotavirus harboring a spike protein with a heterologous peptide reveals a novel role of VP4 in viroplasm stability

Author

Papa, Guido, primary, Vetter, Janine, additional, Seyffert, Michael, additional, Gunasekera, Kapila, additional, De Lorenzo, Giuditta, additional, Wiesendanger, Mahesa, additional, Schraner, Elisabeth M., additional, Reymond, Jean-Louis, additional, Fraefel, Cornel, additional, Burrone, Oscar R., additional, and Eichwald, Catherine, additional

Published
2021
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32. Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion

Author

Papa, Guido, primary, Mallery, Donna L., additional, Albecka, Anna, additional, Welch, Lawrence G., additional, Cattin-Ortolá, Jérôme, additional, Luptak, Jakub, additional, Paul, David, additional, McMahon, Harvey T., additional, Goodfellow, Ian G., additional, Carter, Andrew, additional, Munro, Sean, additional, and James, Leo C., additional

Published
2021
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33. Rotavirus Replication Factories Are Complex Ribonucleoprotein Condensates

Author

Geiger, Florian, primary, Papa, Guido, additional, Arter, William E., additional, Acker, Julia, additional, Saar, Kadi L., additional, Erkamp, Nadia, additional, Qi, Runzhang, additional, Bravo, Jack, additional, Strauss, Sebastian, additional, Krainer, Georg, additional, Burrone, Oscar R., additional, Jungmann, Ralf, additional, Knowles, Tuomas P.J., additional, Engelke, Hanna, additional, and Borodavka, Alexander, additional

Published
2020
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36. Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion

Author

Papa, Guido, primary, Mallery, Donna L., additional, Albecka, Anna, additional, Welch, Lawrence, additional, Cattin-Ortolá, Jérôme, additional, Luptak, Jakub, additional, Paul, David, additional, McMahon, Harvey T., additional, Goodfellow, Ian G., additional, Carter, Andrew, additional, Munro, Sean, additional, and James, Leo C., additional

Published
2020
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38. Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70

Author

Kemp, Steven, Meng, Bo, Ferriera, Isabella ATM, Datir, Rawlings, Harvey, William, Papa, Guido, Lytras, Spyros, Collier, Dami, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Carabelli, Alessandro, Kenyon, Julia, Lever, Andrew, De Marco, Anna, Saliba, Christian, Culap, Katja, Cameroni, Elisabetta, Piccoli, Luca, Corti, Davide, James, Leo, Bailey, Dalan, Robertson, David, Gupta, Ravindra, The COVID-19 Genomics UK (COG-UK) Consortium, Kemp, Steven [0000-0001-7077-6793], Harvey, William [0000-0001-9529-1127], Collier, Dami [0000-0001-5446-4423], Mohamed, Ahmed [0000-0001-9751-1808], and Apollo - University of Cambridge Repository

Subjects
The COVID-19 Genomics UK (COG-UK) Consortium
Abstract

SARS-CoV-2 amino acid replacements in the receptor binding domain (RBD) occur relatively frequently and some have a consequence for immune recognition. Here we report recurrent emergence and significant onward transmission of a six-nucleotide out of frame deletion in the S gene, which results in loss of two amino acids: H69 and V70. We report that in human infections ΔH69/V70 often co-occurs with the receptor binding motif amino acid replacements N501Y, N439K and Y453F, and in the latter two cases has followed the RBD mutation. One of the ΔH69/V70+ N501Y lineages, now known as B.1.1.7, has undergone rapid expansion and includes eight S gene mutations: RBD (N501Y and A570D), S1 (ΔH69/V70 and Δ144) and S2 (P681H, T716I, S982A and D1118H). In vitro , we show that ΔH69/V70 does not reduce serum neutralisation across multiple convalescent sera. However, ΔH69/V70 increases infectivity and is associated with increased incorporation of cleaved spike into virions. ΔH69/V70 is able to compensate for small infectivity defects induced by RBD mutations N501Y, N439K and Y453F. In addition, replacement of H69 and V70 residues in the B.1.1.7 spike reduces its infectivity and spike mediated cell-cell fusion. Based on our data ΔH69/V70 likely acts as a permissive mutation that allows acquisition of otherwise deleterious immune escape mutations. Enhanced surveillance for the ΔH69/V70 deletion with and without RBD mutations should be considered as a global priority not only as a marker for the B.1.1.7 variant, but potentially also for other emerging variants of concern. Vaccines designed to target the deleted spike protein could mitigate against its emergence as increased selective forces from immunity and vaccines increase globally. Highlights ΔH69/V70 is present in at least 28 SARS-CoV-2 lineages ΔH69/V70 does not confer escape from convalescent sera ΔH69/V70 increases spike infectivity and compensates for RBD mutations ΔH69/V70 is associated with greater spike cleavage B.1.1.7 requires ΔH69/V70 for optimal spike cleavage and infectivity

Published
2020

39. Recombinant rotaviruses rescued by reverse genetics reveal the role of NSP5 hyperphosphorylation in the assembly of viral factories

Author

10085637 - Potgieter, Abraham Christiaan, Papa, Guido, Potgieter, Christiaan, Venditti, Luca, Arnoldi, Francesca, Schraner, Elisabeth M., 10085637 - Potgieter, Abraham Christiaan, Papa, Guido, Potgieter, Christiaan, Venditti, Luca, Arnoldi, Francesca, and Schraner, Elisabeth M.

Abstract

Rotavirus (RV) replicates in round-shaped cytoplasmic viral factories, although how they assemble remains unknown. During RV infection, NSP5 undergoes hyperphosphorylation, which is primed by the phosphorylation of a single serine residue. The role of this posttranslational modification in the formation of viroplasms and its impact on virus replication remain obscure. Here, we investigated the role of NSP5 during RV infection by taking advantage of a modified fully tractable reverse-genetics system. A trans-complementing cell line stably producing NSP5 was used to generate and characterize several recombinant rotaviruses (rRVs) with mutations in NSP5. We demonstrate that an rRV lacking NSP5 was completely unable to assemble viroplasms and to replicate, confirming its pivotal role in rotavirus replication. A number of mutants with impaired NSP5 phosphorylation were generated to further interrogate the function of this posttranslational modification in the assembly of replication-competent viroplasms. We showed that the rRV mutant strains exhibited impaired viral replication and the ability to assemble round-shaped viroplasms in MA104 cells. Furthermore, we investigated the mechanism of NSP5 hyperphosphorylation during RV infection using NSP5 phosphorylation-negative rRV strains, as well as MA104-derived stable transfectant cell lines expressing either wild-type NSP5 or selected NSP5 deletion mutants. Our results indicate that NSP5 hyperphosphorylation is a crucial step for the assembly of round-shaped viroplasms, highlighting the key role of the C-terminal tail of NSP5 in the formation of replication-competent viral factories. Such a complex NSP5 phosphorylation cascade may serve as a paradigm for the assembly of functional viral factories in other RNA viruses

Published
2020

41. Recombinant rotaviruses rescued by reverse genetics reveal the role of NSP5 hyperphosphorylation in the assembly of viral factories

Author

García-Sastre, Adolfo, García-Sastre, A ( Adolfo ), Papa, Guido, Venditti, Luca, Arnoldi, Francesca, Schraner, Elisabeth M; https://orcid.org/0000-0003-4608-4812, Potgieter, Christiaan, Borodavka, Alexander; https://orcid.org/0000-0002-5729-2687, Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843, Burrone, Oscar R, García-Sastre, Adolfo, García-Sastre, A ( Adolfo ), Papa, Guido, Venditti, Luca, Arnoldi, Francesca, Schraner, Elisabeth M; https://orcid.org/0000-0003-4608-4812, Potgieter, Christiaan, Borodavka, Alexander; https://orcid.org/0000-0002-5729-2687, Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843, and Burrone, Oscar R

Abstract

Rotavirus (RV) replicates in round-shaped cytoplasmic viral factories, although how they assemble remains unknown. During RV infection, NSP5 undergoes hyperphosphorylation, which is primed by the phosphorylation of a single serine residue. The role of this posttranslational modification in the formation of viroplasms and its impact on virus replication remain obscure. Here, we investigated the role of NSP5 during RV infection by taking advantage of a modified fully tractable reverse-genetics system. A trans-complementing cell line stably producing NSP5 was used to generate and characterize several recombinant rotaviruses (rRVs) with mutations in NSP5. We demonstrate that an rRV lacking NSP5 was completely unable to assemble viroplasms and to replicate, confirming its pivotal role in rotavirus replication. A number of mutants with impaired NSP5 phosphorylation were generated to further interrogate the function of this posttranslational modification in the assembly of replication-competent viroplasms. We showed that the rRV mutant strains exhibited impaired viral replication and the ability to assemble round-shaped viroplasms in MA104 cells. Furthermore, we investigated the mechanism of NSP5 hyperphosphorylation during RV infection using NSP5 phosphorylation-negative rRV strains, as well as MA104-derived stable transfectant cell lines expressing either wild-type NSP5 or selected NSP5 deletion mutants. Our results indicate that NSP5 hyperphosphorylation is a crucial step for the assembly of round-shaped viroplasms, highlighting the key role of the C-terminal tail of NSP5 in the formation of replication-competent viral factories. Such a complex NSP5 phosphorylation cascade may serve as a paradigm for the assembly of functional viral factories in other RNA viruses.IMPORTANCE The rotavirus (RV) double-stranded RNA genome is replicated and packaged into virus progeny in cytoplasmic structures termed viroplasms. The nonstructural protein NSP5, which undergoes a complex hype

Published
2019

42. Identification of a small molecule that compromises the structural integrity of viroplasms and rotavirus double-layered particles

Author

Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843, De Lorenzo, Giuditta, Schraner, Elisabeth M, Papa, Guido, Bollati, Michela, Swuec, Paolo, de Rosa, Matteo, Milani, Mario, Mastrangelo, Eloise, Ackermann, Mathias; https://orcid.org/0000-0001-5268-1467, Burrone, Oscar R, Arnoldi, Francesca, Eichwald, Catherine; https://orcid.org/0000-0003-0001-4843, De Lorenzo, Giuditta, Schraner, Elisabeth M, Papa, Guido, Bollati, Michela, Swuec, Paolo, de Rosa, Matteo, Milani, Mario, Mastrangelo, Eloise, Ackermann, Mathias; https://orcid.org/0000-0001-5268-1467, Burrone, Oscar R, and Arnoldi, Francesca

Abstract

Despite the availability of two attenuated vaccines, rotavirus (RV) gastroenteritis remains an important cause of mortality among children in developing countries causing about 215,000 infant deaths annually. Currently, there are no specific antiviral therapies available. RV is a non-enveloped virus with a segmented double-stranded RNA genome. Viral genome replication and assembly of transcriptionally active double-layered particles (DLPs) take place in cytoplasmic viral structures called viroplasms. In this study, we describe strong impairment of the early stages of RV replication induced by a small molecule known as RNA polymerase III inhibitor, ML-60218 (ML). This compound was found to disrupt already assembled viroplasms and hamper the formation of new ones without the need of de novo transcription of cellular RNAs. This phenotype correlated with reduction in accumulated viral proteins and newly made viral genome segments, disappearance of the hyperphosphorylated isoforms of the viroplasm-resident protein NSP5 and inhibition of infectious progeny virus production. In in vitro transcription assays with purified DLPs, ML showed a dose-dependent inhibitory activity indicating the viral nature of its target. ML was found to interfere with the formation of higher order structures of VP6, the protein forming the DLP outer layer, without compromising its ability to trimerize. Electron microscopy of ML-treated DLPs showed a dose-dependent structural damage. Our data suggest that interactions between VP6 trimers are essential not only for DLP stability but also for the structural integrity of viroplasms in infected cells.IMPORTANCE Rotavirus gastroenteritis is responsible for a large number of infant deaths in developing countries. Unfortunately, in those countries where effective vaccines are urgently needed, the efficacy of the available vaccines is particularly low. Therefore, the development of antivirals is an important goal, as they might complement the available v

Published
2018

43. Identification of a Small Molecule That Compromises the Structural Integrity of Viroplasms and Rotavirus Double-Layered Particles

Author

Eichwald, Catherine, primary, De Lorenzo, Giuditta, additional, Schraner, Elisabeth M., additional, Papa, Guido, additional, Bollati, Michela, additional, Swuec, Paolo, additional, de Rosa, Matteo, additional, Milani, Mario, additional, Mastrangelo, Eloise, additional, Ackermann, Mathias, additional, Burrone, Oscar R., additional, and Arnoldi, Francesca, additional

Published
2018
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44. A Respiratory Syncytial Virus Vaccine Vectored by a Stable Chimeric and Replication-Deficient Sendai Virus Protects Mice without Inducing Enhanced Disease

Author

Wiegand, Marian Alexander, primary, Gori-Savellini, Gianni, additional, Gandolfo, Claudia, additional, Papa, Guido, additional, Kaufmann, Christine, additional, Felder, Eva, additional, Ginori, Alessandro, additional, Disanto, Maria Giulia, additional, Spina, Donatella, additional, and Cusi, Maria Grazia, additional

Published
2017
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46. An inhibitory motif on the 5’UTR of several rotavirus genome segments affects protein expression and reverse genetics strategies

Author

De Lorenzo, Giuditta, Drikic, Marija, Papa, Guido, Eichwald, Catherine, Burrone, Oscar R, Arnoldi, Francesca, De Lorenzo, Giuditta, Drikic, Marija, Papa, Guido, Eichwald, Catherine, Burrone, Oscar R, and Arnoldi, Francesca

Abstract

Rotavirus genome consists of eleven segments of dsRNA, each encoding one single protein. Viral mRNAs contain an open reading frame (ORF) flanked by relatively short untranslated regions (UTRs), whose role in the viral cycle remains elusive. Here we investigated the role of 5'UTRs in T7 polymerase-driven cDNAs expression in uninfected cells. The 5'UTRs of eight genome segments (gs3, gs5-6, gs7-11) of the simian SA11 strain showed a strong inhibitory effect on the expression of viral proteins. Decreased protein expression was due to both compromised transcription and translation and was independent of the ORF and the 3'UTR sequences. Analysis of several mutants of the 21-nucleotide long 5'UTR of gs 11 defined an inhibitory motif (IM) represented by its primary sequence rather than its secondary structure. IM was mapped to the 5' terminal 6-nucleotide long pyrimidine-rich tract 5'-GGY(U/A)UY-3'. The 5' terminal position within the mRNA was shown to be essentially required, as inhibitory activity was lost when IM was moved to an internal position. We identified two mutations (insertion of a G upstream the 5'UTR and the U to A mutation of the fifth nucleotide of IM) that render IM non-functional and increase the transcription and translation rate to levels that could considerably improve the efficiency of virus helper-free reverse genetics strategies.

Published
2016

48. A Single Nucleoside Viral Polymerase Inhibitor Against Norovirus, Rotavirus, and Sapovirus-Induced Diarrhea.

Author

Dycke, Jana Van, Arnoldi, Francesca, Papa, Guido, Vandepoele, Justine, Burrone, Oscar R, Mastrangelo, Eloise, Tarantino, Delia, Heylen, Elisabeth, Neyts, Johan, Rocha-Pereira, Joana, and Van Dycke, Jana

Subjects
ANTIVIRAL agents, VIRAL diarrhea, PREVENTIVE medicine, ROTAVIRUSES, GENOMES, ANIMAL experimentation, CELL lines, COMPARATIVE studies, DIARRHEA, RESEARCH methodology, MEDICAL cooperation, MICROBIAL sensitivity tests, NUCLEOSIDES, PRIMATES, PROTEINS, RESEARCH, RNA viruses, TRANSFERASES, EVALUATION research, RNA virus infections, CHEMICAL inhibitors, PHARMACODYNAMICS
Abstract

A safe and highly efficient antiviral is needed for the prophylaxis and/or treatment of viral diarrhea. We here demonstrate the in vitro antiviral activity of four 2'-C-methyl nucleoside analogues against noro-, rota-, and sapoviruses. The most potent nucleoside analogue, 7-deaza-2'-C-methyladenosine, inhibits replication of these viruses with a 50% effective concentration < 5 µM. Mechanistically, we demonstrate that the 2'-C-methyl nucleoside analogues act by inhibiting transcription of the rotavirus genome. This provides the first evidence that a single viral-diarrhea-targeted treatment can be developed through a viral-polymerase-targeting small molecule. [ABSTRACT FROM AUTHOR]

Published
2018
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49. Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus

Author

Sebastian Strauss, Julia Acker, Guido Papa, Daniel Desirò, Florian Schueder, Alexander Borodavka, Ralf Jungmann, Papa, Guido [0000-0002-5215-0014], Schueder, Florian [0000-0003-3412-5066], Borodavka, Alexander [0000-0002-5729-2687], Jungmann, Ralf [0000-0003-4607-3312], and Apollo - University of Cambridge Repository

Subjects
RNA viruses, Rotavirus, General Immunology and Microbiology, General Neuroscience, infectious disease, microbiology, RNA imaging, chemical biology, General Medicine, Viral Nonstructural Proteins, Virus Replication, General Biochemistry, Genetics and Molecular Biology, Cell Line, Ribonucleoproteins, biochemistry, biomolecular condensates, RNA, RNA, Viral, viruses
Abstract

Funder: Max Planck Institute for Biochemistry, Rotaviruses transcribe 11 distinct RNAs that must be co-packaged prior to their replication to make an infectious virion. During infection, nontranslating rotavirus transcripts accumulate in cytoplasmic protein-RNA granules known as viroplasms that support segmented genome assembly and replication via a poorly understood mechanism. Here, we analysed the RV transcriptome by combining DNA-barcoded smFISH of rotavirus-infected cells. Rotavirus RNA stoichiometry in viroplasms appears to be distinct from the cytoplasmic transcript distribution, with the largest transcript being the most enriched in viroplasms, suggesting a selective RNA enrichment mechanism. While all 11 types of transcripts accumulate in viroplasms, their stoichiometry significantly varied between individual viroplasms. Accumulation of transcripts requires the presence of 3' untranslated terminal regions and viroplasmic localisation of the viral polymerase VP1, consistent with the observed lack of polyadenylated transcripts in viroplasms. Our observations reveal similarities between viroplasms and other cytoplasmic RNP granules and identify viroplasmic proteins as drivers of viral RNA assembly during viroplasm formation.

Published
2023

50. Liquid-liquid phase separation underpins the formation of replication factories in rotaviruses

Author

Runzhang Qi, Julia Acker, Tuomas P. J. Knowles, Nadia A Erkamp, Ralf Jungmann, Sebastian Strauss, Alexander Borodavka, Hanna Engelke, Georg Krainer, Guido Papa, Oscar R. Burrone, Jack P. K. Bravo, William E. Arter, Florian Geiger, Xinyu Wang, Kadi L. Saar, Krainer, Georg [0000-0002-9626-7636], Knowles, Tuomas [0000-0002-7879-0140], Borodavka, Alexander [0000-0002-5729-2687], Apollo - University of Cambridge Repository, Acker, Julia [0000-0002-6422-6514], Papa, Guido [0000-0002-5215-0014], Arter, William E [0000-0002-3615-1885], Jungmann, Ralf [0000-0003-4607-3312], and Engelke, Hanna [0000-0001-9529-9436]

Subjects
Rotavirus, viruses, Viral Nonstructural Proteins, medicine.disease_cause, Virus Replication, EMBO23, Cytoplasmic Ribonucleoprotein Granules, Glycols, Structural Biology, Genes, Reporter, biomolecular condensates, Phosphorylation, Ribonucleoprotein, RNP granules, biology, General Neuroscience, viral genome assembly, RNA-Binding Proteins, Articles, Haplorhini, Propylene Glycol, Microbiology, Virology & Host Pathogen Interaction, Cell biology, Host-Pathogen Interactions, Signal Transduction, Gene Expression Regulation, Viral, Green Fluorescent Proteins, microfluidics, EMBO40, Rotavirus Infections, Article, General Biochemistry, Genetics and Molecular Biology, Cell Line, Organelle, medicine, Animals, Humans, Molecular Biology, General Immunology and Microbiology, Virus Assembly, Osmolar Concentration, RNA, HEK293 Cells, Viral replication, Cytoplasm, Chaperone (protein), biology.protein, Cattle, Protein Processing, Post-Translational
Abstract

Funder: Deutsche Forschungsgemeinschaft (DFG); Id: http://dx.doi.org/10.13039/501100001659, RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein‐RNA condensates that are formed via liquid–liquid phase separation of the viroplasm‐forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon mixing, these proteins readily form condensates at physiologically relevant low micromolar concentrations achieved in the cytoplasm of virus‐infected cells. Early infection stage condensates could be reversibly dissolved by 1,6‐hexanediol, as well as propylene glycol that released rotavirus transcripts from these condensates. During the early stages of infection, propylene glycol treatments reduced viral replication and phosphorylation of the condensate‐forming protein NSP5. During late infection, these condensates exhibited altered material properties and became resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some aspects of the assembly of cytoplasmic rotavirus replication factories mirror the formation of other ribonucleoprotein granules. Such viral RNA‐rich condensates that support replication of multi‐segmented genomes represent an attractive target for developing novel therapeutic approaches.

Published
2021

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